Cool team you got here. I honestly don't play ubers that much, but here are my thoughts.
I think life orb yveltal and primal kyogre are pretty threatening to this team, especially since your groudon has no spdef investment, which means that it takes a lot of damage from ice beams. Yveltal can get free switch-ins when you want to scout for something with aegislash or when you kill your momentum by defogging with giratina, then it proceeds to hit something with dark pulse. Xerneas doesn't take dark aura dpulses that well and when your opponent decides to expect xern and oblivion wing in the next switch-in you have a dead xern (or a xern in range of sucker punch that only has attacking moves). I also agree that ho-oh is decently threatening due to regenerator and free switch-ins against aegislash/primal groudon since you don't pack rock coverage. Mega salamence is scary.
With that in mind I'd suggest a shuca berry tyranitar over aegislash and a new EV spread for primal groudon. Ttar checks yveltal, mega mence and ho-oh, while also providing a way to weaken ekiller for you to revenge kill it with priority/primal groudon. The EV spread for pdon helps you check xerneas (with this EV spread to survive a +2 focus blast and multiple priority everywhere I wouldn't call this a xerneas weak team after replacing aegislash) and avoids the 2HKO from a primal kyogre's ice beam.
I also think stall looks a bit annoying but if you play rayquaza correctly and keep rocks up for lugia it should be an easy win for you.
Hope I helped man, good luck.